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223 Cards in this Set

  • Front
  • Back
Where does transcription initiation start
the TATA box
what hapens at the TATA box
TFIID binds the TATA box
How does TFIID bind the TATA box
by using the TATA boxes binding protein TBP
Once TFIID has bound the TBP and the TATA box what happens
TFIIA and TFIIB are recruited and bind
Once TFIIA and TFIIB are bound, what happens
the TBP distrorts the TATA box
What happens when the TBP distorts the TATA box
it provides a platform to recruit other TFs
Once the TATA box is distorted what TF are recruited
TFIIE TFIIH
What is special a TFIIH
it provides the helicase activity, and requires ATP
Once all these have bound and the RNA Pol II is about to start, what happens
it sheds many of the Transcription factors
How does this happen
by the phosphorlation of it C-terminal tail and by a kinase found in TFIIH
First step in Transcribing Chromatin
Activators help recruit TFa
Which TFs do the activators recruit
Polymerase
How does is this recruit of the Pol by the activators monitiored
The Mediator Complex
How does the Mediator complex associate with the Pol II
by the use of its Cterminal tail
This preformed RNA Poll II-Mediator complex is called
RNA Pol II Holoenzyme
Once the RNA Poll II has shed its initation factors, they are replaced by
elongation factors
What part of the complex brings in these elongation factors
the c terminal tail doamin (brings it all in at the same time)
What is the first thing that happens to the c terminal tail
it has a capping enzyme on the end of its tail
Once the tail has been capped, what hapens
RNA splicing machinery assembles
after RNA splicing machinery has assembles what happens
the factors responsible for cleavage and polyadenylation assemble
The FACT complex is
elongating RNA Pol that must deal with histones in its way
What does the FACT complex have that helps it work through these histones
Spt 16/SSRPI dimer
What does the Spt16/SSRPI dimer do
They work together to disociate an H2A-H2B dimer from the nucleosome
Once this H2A-H2B dimer has been removed, what happens
RNA Pol II can transcribe through the nucloesome
Then what happens
The nucleosome is reassembled
How
With Spt16/SSRPI and with help from SPT6
Capping involves adding a lot of ? to ? end of the Cterminal tail domain
Methyl groups
5' end
Polyadenylation involves adding a lot of ? to the ? end of the newly sytnthesized RNS
Adenines
3' end
Once the end of a gene is reached RNA Pol II will
signal the transfer of polyadenylation enzymes to the RNA
The first step in the process of signaling the polyadenlyation enzymes to the RNA is
two enzymes, cleavage and polydenylation specifity factor (CPSF) and cleavage stimulation factor (CstF) move from the CTD to the Poly-A sequence
Once these CPSF and CstF are recuited to the RNA what happens
the RNA is cleaved from the RNA Pol II
After the RNA is cleaved, what happens
Poly-A polymerase (PAP) add several more adenines to the 3' end of the RNA
Once a lot of adenines have been added, what happens
Poly-A binding proteins bind to the poly-A stretch
LECTURE 16
LECTURE 16
The more introns you have,
the more complex the organism
Why is this the case
bc the more introns you have, the more control you have during splicing so it is a more complex organism
intron exon boundary
site that will be spliced
5' splice site
boundary at the 5' end of the intron
what is cut first
the 5' intron/exon boundary
3' binding site
site at the 3' end of the intron exon
what binds the 3' end
the freed 5' end
branch point site
point where the spliced 5' intron make the lariet
Where is the branch point site found
entirely in the Intron
First step in splicing
the 2'-OH group from the A site attacks the Phosphate group of the G site
What is a result of this
the freed 5' end of the intron is joined to the branch site
After that, what happens
The 3'-OH group of the freed exon attacks the Phosphate group of the 3' splice site
What is the result
one intron lariet
and one spliced together exon
When you see the A site you know you are where
In the Middle
When you see the G site you know you are where
Start
What is it called when two exons from different RNAs get spliced together
Trans-splicing
What is the result of trans-splicing
There is a Y-shaped structure insted of a lariet
What does the Splicesome do
It mediates the formation of the lariet and exons
What is the first step in this
Branch Point Binding Protein (BBP) protein binds the A site
What binds the 5' splice site
U1
Once U1 is bound, what happens the BBP
It is replaced by U2
What does U2 do
Distorts the A site
What helps BBP bind to the A site
U2FA
Once U2 replaces BBP what happens
U4 U5 and U6 join the complex
How are the U4 U5 U6 are associated together
U4 and U6 are more tightly held together then U5
What is the main function of U4 U5 and U6
they bring U1 and U2 together (5' splice site and branch site)
Once U1 and U2 are brought together by U4 U5 U6, what happens
U1 leaves
When U1 leaves, what happens
U6 replaces it one hte 5; site
Once U6 is one the 5' site, what happens
U4 leaves
what does U4 leaving allow
It allows U6 and U2 to interact
When you U6 and U2 interact, what happens
It generates the active site and the 5' intron exon boundary is spliced
Then U5
helps bring together the exons
Pre-mRNA splicesome is the
Most common
Group II self-splicing are different because they
do not use a splicesome
Instead they
simple fold on themselves
Group I self splicing do not use
a splicesome
Instead group I
bind guanine
Group I self splicing is
RARE
One way that the accuracy of splice-site selection can be enhanced
Loading splicing machinery during transcription
What would do this, and how does it help improve
CTD
The transcriptional loading of splicing proteins reduces the likely hood of an exon being skipped
Another way that accuracy of splice-site can be enhanced
Proteins that only splice sites close to exons are recognized
These proteins are called
SR proteins
Where do these SR proteins bind
Exonic Splicing Enhancers (ESEs)
And what do these SR proteins do
recruit U2FA to the 3' splice site and U1 to the 5' splice site
U1 U2 U3 U4 U5 U6 are all examples of
snRNPs
U1
binds the 3' splice site
U2
Binds the branch site
U6
brings U1 and U2 together
U4
leaves so that U6 and U2 can from the active site
U5
Helps the exons to bind
LECTURE 17
LECTURE 17
Synonyms are
codons that code for the same amino acid
What does degeneracy mean
More than 1 codon can code for the same amino acid
Mutations in the first nucleotide will often give
similar if not the same amino acid
Pyrimidines in the second position mostly code for
hydrophobic amino acids
Purines in the second position mostly code for
polar amino acids
Transition mutations in the 3rd poition
rarely change the amino acid
Does do they mean by Wobble
Purified tRNA can bind more than one codon
In some tRNAs an additional anticodon base was found
inosine
What can Inosine pair with
A U C
How does the wobble concept work
The 5' end of the anti codon is not as restricted as the other two allowing it to form hydrogen bonds with several bases at the 3' end of the codon
Which end of the anti codon is mist exposed:
5' end
Where is the 3' end
towards the top and it is in the middle of a series of base stacking interactions so it is more restricted
3 Rules that Govern the Genetic Code
-Codons are read by Ribosomes in the 5'-3' direction
-Codons are non overlapping and mRNA contains no gaps
-mRNA is translated in a fixed reading frame (from first AUG)
Three kinds of Point mutation
Missense
Nonsense
Frameshirt
Missense mutations
changes a single base, which changes a single amino acid
Do missense mutation effect the length of the polypeptide
No
Nonsense mutations
change a single base, which changes an amino acid to a stop codon
Do nonsense mutations effect length
Yes
Frameshift mutations
insert or delete one or more bases, which changes the reading frame
Do frameshift mutations effect the length
maybe, you may encode for a stop codon sooner
Two ways mutations can be reversed
Reverse (back) mutations
Supressor mutations
Reverse (back mutations)
just go to where the altered nucleotide is and change it back
Supressor mutations
mutations in another region of DNA can supress the harmful effect of the original mutation
LECTURE 18
LECTURE 18
What does the ribosome do again
corrdinates recognition of the mRNA by the tRNA and forms bonds between individual amino acids on the gorwin peptide chain
Open reading frames (ORFs) are
the regions of mRNA that are composed of non overlapping condons
The most real ORF has
the longest strand that has both a stop and start codon
The ribosome is composed of two parts
Small subunit
LArge subunit
The small subunit is the
decoding center (where tRNAs read the mRNA codons)
The large subunit is the
peptidyl transferase center (where peptide bonds are formed)
Prokaryotic ribosome is
70s (30-Small,40-Large)
The Eukaryotic ribosome is
80s (40-Small,60-Large)
In Prokaryotes how do they recruit the ribosome
by the ribosome binding sites on their ORFs
In Eukaryotes how do they recruite the ribosome
by the use of their 5' cap on the 5' end
Translation is slower in Pro or Euk?
Eukaryotes
why
because translation and transcription take place in different ares of the cell
where does translation take place
cytoplasm
where does transcription take place
nucelus
Why is it faster in prokaryotes
transcription and translation machinery are located in the same compartment
The compostion of the ribosome is split nearly in half with
Proteins and rRNA
The proteins are ? so there are ? or them
smaller
more
The rRNAs are? so there are ? of them
larger
less
First step in the Ribosome association and dissaciation process
mRNA and initiator tRNA bind to the small Ribosome subunit
after the mRNA/tRNA/Small subunit is formed
it recuits a large subunit
once the large subunit has formed
initioation begins
As the Ribosome moves from codon to codon
More initiator tRNA are added to elongate the growing polypeptide chain
How many ribosomes can translate a single mRNA
MANY
an mRNA bearing multiple ribosomes is caled
Polyribosome or polysome
Since many ribosome can translate one mRNA, this means that mRNA
do not have to be abundant
New amino acids are added to the
C(carbon)-terminus of the growing poly peptide chain
The substrates for each new amino acid addition are charged by two species of tRNA
Aminoacyl-tRNA
Peptidyl-tRNA
The peptidyl-tRNA is located
at the C-Terminus of the polypeptide
What does the aminoacytl tRNA do
it attack the peptide-tRNA
how does the aminoactl tRNA attack the peptidyl tRNA
in Amine group (N) attacks the attacks the carbonyl (C) group of the peptidyl tRNA
what is the result
a new peptide bond is formed
This means proteins must grow from the ? to the ? terminus
N to the C
Ribosomes have 3 binding sites
A site: Aminoacyl-tRNA site
P site: Peptidyl-tRNA site
E site: Exit site
During the elongation process, which site is the first site occupied?
P site
What is the second site occupied
A site
LECTURE 19
LECTURE 19
First step n general prokaroytic translation
all machinery is recruitted (mRNA, tRNA initiato complex, Small ribosome)
Secdon step
tRNA must be loaded to the P site
Third
large ribosome binds and it is positioned over a start codon
WHat does IF3 do
It binds the E site and prevents the large ribosome from binding
What does IF1 do
blocks the A site and prevents new tRNA from binding
What does IF2 do
IF2 is a GTPase that interacts with IF1 and the initiator tRNA to help bind the fMet-tRNA. and it helps block the A site
First step
Initiator tRNA is recruitted
where does this initiator tRNA bind
the P site
After the initiator tRNA is bound and it finds a start codon what happens
Once it binds a start codon IF3 is released
what happens when IF3 is released
a large ribosome can now bind the subunit
What happens when the large subunit joins
it stimulates IF2 to hydrolize its GTP
What is the result of IF2 hydrolizing its GTP
If2 and IF1 are released
What happens when IF1 and IF2 are released
Then A site is now open and can bind new tRNA
In Eukaroytes there are ? more steps
A LOT
eIF1/3/5 all block the ? site and prevent the ?
E site
the large ribosome from binding
eIF2-GTP/Met-tRNA complex is loaded to the
P site
What does EF-Tu do
it escorts the aminoacyl-tRNA to the ribosome
How does it do this
EF-Tu utilizes GTP
first step in this process
The EF-Tu-GTP binds the 3' end of the aminoacyl tRNA
What does this EF-Tu-GTP/Aminoacyl tRNA do next
it takes the aminyl tRNA to the A site
Once the complex is at the A site what happens
The EF-tu-GTP comes in contact with the factor binding center
What does this contact do
Causes the EF-Tu to hyrolsize its GTP and dissociate from the amincyl tRNA
Translocation in the ? subunit comes before translocation in the ? subunit
Large comes before
Small
During the hyrbid state, once the peptide transfer is done, the ? site is open
A
What binds the A site
EF-G
EF-G bind the A site only when
It has GTP with it
This EF-G-ATP complex binds then A site, then what
The EF-G-GTP comes in contact with the factor binding center
This contact with the factor binding center causes the EF-G-ATP to do what
hydrolsize its GTP into GDP
What happens when the GTP is hydrolosizes
it changes the shape of the EF-G
The shape change in the EF-G causes what
the EF-G to reach down and scoop and translocate the A site tRNA
LECTURE 20
LECTURE 20
Gene expression is controled by
extracellular signals
If there are no signals
RNA Pol will bind weakly
If there are repressive signals
repressor protein binds the operator site and there is no transcription
If there are activating signals
Activator proteins bind the activating site
In allostery the activator
produces an allosteric change )shape) and it activates transcription
in the Lac Operon, if lactose is absent
The lac Operon will be OFF
If glucose is present
The Lac Operon will be OFF
the lac Z gene
cleaves lactose to produce glucose
The lac Y gene
encodes lactose permease and incorpporates itself into the cell
The lac A gene
encodes thiogalactoside and rids the cell of toxins
Where is the Lac Repressor found and what encodes it
Operator site
lacI
When are Lac z, Y, and A present
in high levels of lactose
The CAP site
mediates the effect of glucose
The CAP will bind only where and only when
The CAP site
there is no glucose
Lac Repressor binds where and only when
Operator site
No lactose
If there is Glucose and Lactose,
The CAP and Repressor do not bind
When the CAP and Repressor do no bind, this is called
Basal Transcription
What part of the RNA Pol binds to the CAP site
The CTD
What happens when they bind
RNA Pol is activated
LECTURE 21
LECTURE 21
3 Main roles of the tro operon
regulate levels of tryptophan
Sense the levels
Synthesize enzymes when levels are too low
The repressor bind the trp operon where
the operator site
When does it bind and repress trp?
When trp levels are high
When there is high trp
Repressor is on
When there is low trp
repressor is off
So lactose is a ? of transcription while trypophan is a ?
Promotor
Repressor
regions 3 and 4 on the trp operon are important because
They can form a hairpin structure
what does the formation of this hairpin structure do
stops transcription
what is this hairpin structue called
attenuator site
When there are moderate to high levels of trp
sites 3 and 4 form a hairpin structure
What does the formation of this hairpin structure do
Does not alow the ribosome to move along and therefore does not transcribe genes
During low levels of trp
sites 2 and 3 form the hairpin
What happens when sites 2 and 3 form the hairpin
The DNA Pol come apart and then attachs the to other side of the hairpin and continues transcribing
Two different phage life cycles
lysogenic
lytic
Which gene is pro-lytic
cro
which gene is pro-lysogenic
cI
Which promotors are pro-lytic
Pr and Pl
Which promotors are pro-lysogenic
Prm
Pl and Pr make transcription
turn on
why
because the lytic stage is active and the lysogenic stage is repressed
Pl and Pr produce a lot of
cro
Prm produces a lot of
cI
cI is called the
phage repressor , BUT it can also be an activator
as a repress it bind at the ? and therefore ?
Opperator
Blocks RNA Pol
As an activator cI works like
CAP and recruits RNA Pol
cro works only as a
repressor
and cro binds DNA as A
dimer